Documentation: Notes not copied

[bangerth]

There are ~46 occurrences of \note in the latex sources, which in the conversion to sphinx were all converted as

    <div class="center">

    </div>

That is, not only is the markup wrong, but the actual note text is missing. We will need to go through all of these by hand, copy the text from the latex sources, convert them to markdown, and make sure that the result renders correctly.

The complete list is here:

> grep -r '\\note' doc/manual/manual.tex `find cookbooks/ benchmarks/ | grep .tex | grep -v parameters.tex`
doc/manual/manual.tex:% be able to use \note environments with a box around the text
doc/manual/manual.tex:\newcommand{\note}[1]{
doc/manual/manual.tex:\note{\aspect{} is a community project. As such, we encourage contributions
doc/manual/manual.tex:\note{\aspect{} will only solve problems relevant to the community if we get
doc/manual/manual.tex:\note{For mantle convection simulations, it is often convenient to work with
doc/manual/manual.tex:\note{By default, \aspect{} uses the full pressure in the equations, and only prescribing
doc/manual/manual.tex:\note{The adiabatic surface temperature is often chosen significantly
doc/manual/manual.tex:\note{As has hopefully become clear from the discussion above, the
doc/manual/manual.tex:\note{Historically, the mantle convection community has typically used
doc/manual/manual.tex:\note{Our energy equation is formulated in terms of $T$, while in the literature, the equation
doc/manual/manual.tex:\note{\aspect{} does not solve the equations in the way described in this paragraph,
doc/manual/manual.tex:\note{This is the default approximation \aspect{} uses to model compressible convection,
doc/manual/manual.tex:\note{\textbf{The stress tensor approximation.}
doc/manual/manual.tex:\note{In the current version of \aspect{}, it is the responsibility of the user to select a
doc/manual/manual.tex:\note{Here, we do not use the visco-elasto-plastic rheology of the \cite{KMK2013} formulation.
doc/manual/manual.tex:\note{If you own other finished containers that you want to keep use
doc/manual/manual.tex:\note{As noted in Section~\ref{sec:non-dimensional}, \aspect{} can be
doc/manual/manual.tex:\note{It goes without saying that if you make significant modifications to the
doc/manual/manual.tex:\note{You can select other formats for output than VTU, see the run-time
doc/manual/manual.tex:\note{After setting output to a file, \textit{all} following plot commands will
doc/manual/manual.tex:\note{An alternative would be if every processor directly writes its own files
doc/manual/manual.tex:\note{It is not imperative that the parameters selected in the input file are
doc/manual/manual.tex:\note{In cases where a parameter requires a significant amount of text, you can
doc/manual/manual.tex:\note{Not all text replacements are unique, and the structure of input files
doc/manual/manual.tex:\note{The input files discussed in the following sections can generally be
doc/manual/manual.tex:\note{It is of course possible to set up input files for computations
doc/manual/manual.tex:\note{Complex projects built on \aspect{} often require plugins of more than
doc/manual/manual.tex:\note{If you choose to compile your plugins into a shared library yourself, you
doc/manual/manual.tex:\note{For reasons that have to do with the way the
doc/manual/manual.tex:\note{Not all text replacements are unique, and the structure of plugin files
doc/manual/manual.tex:\note{Chances are that if you think about using the signal mechanism, there is
doc/manual/manual.tex:\note{Neither this manual, nor the documentation in \aspect{} makes much of an
doc/manual/manual.tex:\note{\aspect{} is a community project. As such, we strongly encourage contributions
cookbooks/composition_active_particles/doc/composition_active_particles.tex:\note{\aspect{}'s particle implementation is in a preliminary state. While the accuracy and scalability of the implementation is benchmarked, other limitations remain. This in particular means that it is not optimized for performance, and more than a few thousand particles per process can slow down a model significantly. Moreover, models with a highly adaptive mesh and many particles do encounter a significant slowdown, because \aspect{} only considers the number of degrees of freedom for load balancing across processes and not the number of particles. Therefore processes that compute the solution for coarse-grid regions have to process many more particles than other processes. Additionally, the checkpoint/restart functionality for particles is only implemented in models with a constant number of processes before and after the checkpoint and when the selected particle properties do not change. These limitations might be removed over time, but for current models the user should be aware of them.}
cookbooks/finite_strain/doc/finite_strain.tex:\note{In this section, following \cite{Becker2003, dahlen1998theoretical}, we denote the velocity gradient tensor as $\mathbf G$, where $\mathbf G = \nabla \mathbf u^T$,
cookbooks/finite_strain/doc/finite_strain.tex:\note{In this model we present the use of multiple compositional fields for other purposes than chemical composition.
cookbooks/steinberger/doc/steinberger.tex:\note{If the model takes too long to run, increase the minimum viscosity.}
cookbooks/platelike-boundary/doc/platelike-boundary.tex:\note{While you can enter most any expression into the parser for these
cookbooks/convection-box/doc/convection-box.tex:\note{If you want to run a version of this cookbook that uses Earth-like rather than nondimensional parameters, and that includes particles that visualize the flow field, see Section~\ref{sec:cookbooks-running-a-model}.}
cookbooks/geomio/doc/geomio.tex:\note{This cookbook is based on a developer version of geomIO from July 2016. In the meantime, the development of
cookbooks/geomio/doc/geomio.tex:\note{geomIO currently only supports the latest stable version of Inkscape (0.91), and other versions might not
cookbooks/geomio/doc/geomio.tex:\note{The page of your drawing in Inkscape should already have the extents (in px) that you later want to use in your model (in m).}
cookbooks/continental_extension/doc/continental_extension.tex:\note{It is important to consider that the non-linearity of visco-plastic rheologies and mesh-dependence of brittle shear bands make lithospheric deformation models highly sensitive to a large number of parameters. In order to ensure the conclusions drawn from a series of numerical experiments are robust, one should complete a sensitivity test for a large range of parameters including grid resolution, model geometry, boundary conditions, initial composition and temperature conditions, material properties, composition discretization, CFL number and solver settings. If you are new to modeling lithospheric processes, a reasonable starting point is to try and reproduce results from a relevant previous study and then perform a sensitivity test for the parameters listed above. While highly time consuming, completing this procedure will prove invaluable when you design and assess the results of your own numerical study.}
cookbooks/shell_simple_2d/doc/shell_simple_2d.tex:\note{Having described everything to \aspect{}, you may want to view the video linked
cookbooks/morency_doin_2004/doc/morency_doin_2004.tex:\note{\cite{MD04} defines the second invariant of the strain rate in a nonstandard way.
cookbooks/morency_doin_2004/doc/morency_doin_2004.tex:\note{The viscosity profile in Figure 1 of \cite{MD04} appears to be wrong. The published

[MFraters]

I think this is resolved. At least, searching for <div class="center"> doesn't yield any results. Can you confirm @bangerth

[bangerth]

Yes, I spot checked this and now see that all of the places I checked look like this:

:::{note}
This cookbook is based on a developer version of geomIO from July 2016. In the
meantime, the development of geomIO continued, and there is now a publication
{cite}`bauville:baumann:2019` that describes its features and how they can be
used in more detail.
:::